The boot list is stored in the firmware, the firmware is just like the bios on a PC.
The process is just the same, you must tell the firmware where to look for the boot device.
In AIX you can use the bootlist command to display or update the bootlist in the system firmware.

You are correct, if the battery dies there may be a problem booting.

Just like going in to the bios on a pc to correct a boot list after the battery died, on an AIX machine you can use SMS to correct the boot list.

Typically most people have the rootvg on local, internal, disks and any datavg's on SAN disks. This way if the SAN fails, the machine is still bootable, even if it cannot do any work because the SAN is offline.

You will probably also find the internal disks are slightly faster than SAN disks, this is useful for fast access to the operating system files and paging space.

Without a lot more information about your system and SAN configuration and testing of your specific setup there is no way to tell which would be best for you.

If you only have a small amount of space on the internal disks or one fiber card I'd leave things as they are, but check to see if the system can boot from the SAN disks, just so you know what you'll need to do to recover the system if the internal boot disk fails.